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Title: Thermodynamic Studies on DNA Unzipping
Researcher: Singh, Amar
Guide(s): Singh, Navin
Keywords: Biological Science, DNA Unzipping
University: Birla Institute of Technology and Science
Completed Date: 2015
Abstract: Prediction of DNA duplex stability and thermodynamics is invaluable for many molecular biology applications. Sequence dependent stability of duplex DNA plays a major role in fundamental processes of the newlineliving cell, such as replication and transcription. In these fundamental processes, DNA must undergo dynamical and structural changes.Since these processes require a local opening of the DNA molecule, they resemble DNA denaturation, or DNA melting, which is a considerably simpler process to study theoretically and experimentally. For this, In-vitro we need to understand how the CELL environment affects the equilibrium properties and the dynamics of the DNA molecule. After the discovery of the helix structure, the attention was for a long time directed at the DNA denaturation, specifically the effect of chain sequence and length. In past few years a particular interest has been newlinedevoted to the study of mechanical strand separation shading light on the role of thermal fluctuations and sequence. In this work, the denaturation and mechanical unzipping of DNA were explored by numerical newlinesimulations applying the PBD model. Although DNA dynamics has gained increased interest during the last decades, there is still a need of more insight and knowledge within this field. This thesis work contains the first quantitative study of DNA denaturation as well as the DNA unzipping in concentrated and crowded solutions through the well-known PBD mesoscopic model. We study the thermal melting of short heterogeneous DNA sequences as well as the complete unzipping of and#955;-phase DNA at different salt conditions. We also study the unzipping of short DNA molecules having defects or mismatches at different newlinelocations in the sequence. The outcome elucidate the role of loop entropy and bubble formation in opening of DNA molecules. In case of force induced unzipping not only the magnitude of the applied force is important, but the nature of force, how and where force is applied,is also important in the unders
Pagination: 159p.
Appears in Departments:Biological Science

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